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Nucleic Acids Research Advance Access published online on October 16, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm763
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals

Yong Seok Lee1,2, Jeongsu Oh2, Young Uk Kim2, Namchul Kim2, Sungjin Yang2 and Ui Wook Hwang1,*

1Department of Biology, Kyungpook National University, Daegu 702-701 and 2Korean Bioinformation Center, KRIBB, Daejeon 305-806, Korea

*To whom correspondence should be addressed. Tel: 82 53 950 5911; Fax: 82 53 950 6809; Email: uwhwang{at}knu.ac.kr The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Received August 14, 2007. Revised September 5, 2007. Accepted September 11, 2007.

Mitome is a specialized mitochondrial genome database designed for easy comparative analysis of various features of metazoan mitochondrial genomes such as base frequency, A+T skew, codon usage and gene arrangement pattern. A particular function of the database is the automatic reconstruction of phylogenetic relationships among metazoans selected by a user from a taxonomic tree menu based on nucleotide sequences, amino acid sequences or gene arrangement patterns. Mitome also enables us (i) to easily find the taxonomic positions of organisms of which complete mitochondrial genome sequences are publicly available; (ii) to acquire various metazoan mitochondrial genome characteristics through a graphical genome browser; (iii) to search for homology patterns in mitochondrial gene arrangements; (iv) to download nucleotide or amino acid sequences not only of an entire mitochondrial genome but also of each component; and (v) to find interesting references easily through links with PubMed. In order to provide users with a dynamic, responsive, interactive and faster web database, Mitome is constructed using two recently highlighted techniques, Ajax (Asynchronous JavaScript and XML) and Web Services. Mitome has the potential to become very useful in the fields of molecular phylogenetics and evolution and comparative organelle genomics. The database is available at: http://www.mitome.info.


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